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- PDB-6goj: X-ray structure of the adduct formed upon reaction of lysozyme wi... -

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Basic information

Entry
Database: PDB / ID: 6goj
TitleX-ray structure of the adduct formed upon reaction of lysozyme with a Pt(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated triphenylphosphonium cation
ComponentsLysozyme C
KeywordsHYDROLASE / protein-metallodrug interaction / platinum-based drug / N-pyridylbenzimidazole bidentate ligands / stacking / non covalent bond
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / : / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMerlino, A. / Ferraro, G.
CitationJournal: Dalton Trans / Year: 2018
Title: Exploring the interactions between model proteins and Pd(ii) or Pt(ii) compounds bearing charged N,N-pyridylbenzimidazole bidentate ligands by X-ray crystallography.
Authors: Ferraro, G. / Mansour, A.M. / Merlino, A.
History
DepositionJun 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9167
Polymers14,3311
Non-polymers5856
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-71 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.108, 78.108, 37.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-381-

HOH

21A-394-

HOH

31A-410-

HOH

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 20% ethylene glycol 0.6 M sodium nitrate 0.1 M sodium acetate pH 4.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→55.23 Å / Num. obs: 5705 / % possible obs: 97.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.3
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.755 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dpx

1dpx


Resolution: 2.25→55.23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.856 / SU B: 8.326 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.3 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27886 293 5.2 %RANDOM
Rwork0.17152 ---
obs0.17693 5396 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.692 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å2-0 Å2
2--0.6 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: 1 / Resolution: 2.25→55.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 12 111 1124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191079
X-RAY DIFFRACTIONr_bond_other_d0.0020.02992
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9211469
X-RAY DIFFRACTIONr_angle_other_deg1.03132256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5722.03754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57115178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3581515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021299
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02295
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5532.675535
X-RAY DIFFRACTIONr_mcbond_other1.5552.673534
X-RAY DIFFRACTIONr_mcangle_it2.3854.018674
X-RAY DIFFRACTIONr_mcangle_other2.3844.021675
X-RAY DIFFRACTIONr_scbond_it2.0962.922543
X-RAY DIFFRACTIONr_scbond_other2.0872.909538
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4874.29792
X-RAY DIFFRACTIONr_long_range_B_refined4.85121.5291284
X-RAY DIFFRACTIONr_long_range_B_other4.71321.3521265
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.251→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 21 -
Rwork0.192 383 -
all-281 -
obs--94.61 %

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